ALBERT

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.

Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.

Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.

Description: Atlantic halibut ( Hippoglossus hippoglossus ) have a long history of exploitation in the Northwest Atlantic and have gone through several periods of high biomass followed by a population crash. An assessment model using data collected on the Scotian Shelf and southern Grand Banks shows that the population peaked in 1984, then decreased sharply to a low in 1993. Several management measures were taken during the decline, including reductions in total allowable catch and a minimum size limit. Concurrently, removals by the otter trawl fishery were drastically reduced following the collapse of the cod ( Gadus morhua ) fishery. In 2003, recruitment increased and continued to be high for 6 years. Fishing mortality rates were moderate in the late 1990s and 2000s and the population increased. By 2009, the Atlantic halibut population was highly productive with both high biomass and high levels of recruitment. The coincidence in the timing of population recovery and management actions indicates that effective management contributed to the recovery of Atlantic halibut.

Description: Using the Low Dispersion Survey Spectrograph 3 at the Magellan II Clay Telescope, we target candidate absorption host galaxies detected in deep optical imaging (reaching limiting apparent magnitudes of 23.0–26.5 in g , r , i , and z filters) in the fields of three QSOs, each of which shows the presence of high metallicity, high $N_{\rm H\,\small {i}}$ absorption systems in their spectra (Q0826-2230: z abs = 0.9110, Q1323-0021: z abs = 0.7160, Q1436-0051: z abs = 0.7377, 0.9281). We confirm three host galaxies at redshifts 0.7387, 0.7401, and 0.9286 for two of the Lyman α absorption systems (one with two galaxies interacting). For these systems, we are able to determine the star formation rates (SFRs); impact parameters (from previous imaging detections); the velocity shift between the absorption and emission redshifts; and, for one system, also the emission metallicity. Based on previous photometry, we find these galaxies have L 〉 L *. The [O ii ] SFRs for these galaxies are in the range 11–25 M  yr –1 (uncorrected for dust), while the impact parameters lie in the range 35–54 kpc. Despite the fact that we have confirmed galaxies at 50 kpc from the QSO, no gradient in metallicity is indicated between the absorption metallicity along the QSO line of sight and the emission line metallicity in the galaxies. We confirm the anticorrelation between impact parameter and $N_{\rm H\,\small {i}}$ from the literature. We also report the emission redshift of five other galaxies: three at z em 〉 z QSO , and two ( L 〈 L *) at z em 〈 z QSO not corresponding to any known absorption systems.

Description: Factors driving the distribution of marine microorganisms are widely debated and poorly understood. Recent studies show that free-living marine microbes exhibit geographical patterns indicative of limited dispersal. In contrast, host-associated microbes face a different set of dispersal challenges, and hosts may function as habitat ‘islands’ for resident microbial populations. Here, we examine the biogeographical distributions of planktonic and adjacent coral-associated bacterial communities across the Hawaiian Archipelago, Johnston Atoll (~1400 km southwest of Hawaii) and American Samoa in the Pacific Ocean and investigate the potential underlying processes driving observed patterns. Statistical analyses of bacterial community structure, determined using a small-subunit ribosomal RNA gene-based approach, showed that bacterioplankton and coral-associated bacterial communities were distinct, and correlated with geographical distance between sites. In addition, biogeographical patterns of bacterial associates paralleled those of their host coral Porites lobata , highlighting the specificity of these associations and the impact that host dispersal may have on bacterial biogeography. Planktonic and coral-associated bacterial communities from distant Johnston Atoll were shown to be connected with communities from the center of the Hawaiian Archipelago, a pattern previously observed in fish and invertebrates. No significant correlations were detected with habitat type, temperature or depth. However, non-distance-based geographical groupings were detected, indicating that, in addition to dispersal, unidentified environmental factors also affected the distributions of bacterial communities investigated here.

Description: Genome-wide association studies in Crohn's disease (CD) have identified 140 genome-wide significant loci. However, identification of genes driving association signals remains challenging. Furthermore, genome-wide significant thresholds limit false positives at the expense of decreased sensitivity. In this study, we explored gene features contributing to CD pathogenicity, including gene-based association data from CD and autoimmune (AI) diseases, as well as gene expression features (eQTLs, epigenetic markers of expression and intestinal gene expression data). We developed an integrative model based on a CD reference gene set. This integrative approach outperformed gene-based association signals alone in identifying CD-related genes based on statistical validation, gene ontology enrichment, differential expression between M1 and M2 macrophages and a validation using genes causing monogenic forms of inflammatory bowel disease as a reference. Besides gene-level CD association P -values, association with AI diseases was the strongest predictor, highlighting generalized mechanisms of inflammation, and the interferon- pathway particularly. Within the 140 high-confidence CD regions, 598 of 1328 genes had low prioritization scores, highlighting genes unlikely to contribute to CD pathogenesis. For select regions, comparably high integrative model scores were observed for multiple genes. This is particularly evident for regions having extensive linkage disequilibrium such as the IBD5 locus. Our analyses provide a standardized reference for prioritizing potential CD-related genes, in regions with both highly significant and nominally significant gene-level association P -values. Our integrative model may be particularly valuable in prioritizing rare, potentially private, missense variants for which genome-wide evidence for association may be unattainable.

Description: We present photometric and spectroscopic measurements of 53 QSO–galaxy pairs from the Sloan Digital Sky Survey (SDSS), where nebular emission lines from a 0 〈 z 〈 0.84 foreground galaxy are detected in the fibre spectra of a background QSO, bringing the overall sample to 103 QSO–galaxy pairs detected in the SDSS. We here study the nature of these systems. Detected foreground galaxies appear at impact parameters between 0.37 and 12.68 kpc. The presence of oxygen and Balmer emission lines allows us to determine the emission line metallicities for our sample, which are on average supersolar in value. Star formation rates for our sample are in the range 0.01–12 M  yr –1 . We utilize photometric redshift fitting techniques to estimate the M * values of our galaxies (log M * = 7.34–11.54), and extrapolate this relationship to those galaxies with no imaging detections. Where available, we measure the absorption features present in the QSO spectrum due to the foreground galaxy and the relationships between their rest equivalent widths. We report an anticorrelation between impact parameter and E ( B  –  V ) ( g  –  i ) , as well as a correlation between galaxy colour ( u  –  r ) and E ( B  –  V ) ( g  –  i ) . We find that our sample is one of late-type, star-forming galaxies comparable to field galaxies in a similar redshift range, providing important clues to better understand absorption systems. These galaxies represent a sample of typical galaxies in the local Universe for which abundances, extinction, morphology, and absorption properties may be measured using background QSOs with great potential for follow-up observations.

Description: The Asian copepod Pseudodiaptomus forbesi has conspicuously invaded the Columbia River, but its feeding behavior is poorly understood. We conducted feeding experiments with P. forbesi and natural assemblages of microplankton collected from three sites in the Columbia River. Pseudodiaptomus forbesi primarily consumed diatoms, ciliates, flagellates and dinoflagellates, exhibiting a general preference for diatoms and ciliates, and an avoidance of chlorophytes and cyanobacteria. These results suggest potential competition with native copepods and other food web impacts.

Description: We have improved upon our previous search technique of systematically searching quasi-stellar object (QSO) spectra for narrow galactic Hα emission, which indicates a foreground galaxy within the Sloan Digital Sky Survey (SDSS) spectral fibre. We now search for Hα plus eight other galactic emission lines in the same manner. We have scanned the SDSS data release 7 (DR7) QSO catalogue spectra searching for these emission lines. Here, we present our sample which focuses on the redshift range z  〈 0.401 where galactic Hα is detectable in the SDSS spectra. This has revealed 27 unique galaxies on top of QSOs (GOTOQs). We have deblended the QSOs from the respective galaxies and determined the photometric properties of these systems. We find upon deblending that most of the galaxies are primarily blue, late-type galaxies with colours in the range –0.71 〈 ( u  –  r ) 〈 2.07. We find a slight anticorrelation between reddening and impact parameter [ E ( B  –  V ) ( g  –  i ) versus b ]. The galaxies have average star formation rates of 0.01–1 M  yr –1 , with an average of 0.6 M  yr –1 . They range in z from 0 to 0.4 and in stellar luminosity from about 0.01 L * to 3.0 L *. They are foreground to QSOs of brightness 17.4–20.4 mag ( r band) with the impact parameters of 1–10 kpc. They represent a fair sample of typical galaxies for which it should be possible to determine accurately various quantities (e.g. abundances, dust extinction and Faraday rotation) using follow-up analysis of the background QSOs. Where present, Ca ii 3934 (K) and Na i 5892 (D2) absorption lines were also measured in the QSO spectrum. We find 15 systems with Ca ii K absorption and 6 with Na i D2 absorption. We find no trends relating the equivalent widths of these lines to impact parameter or reddening of the background QSO. Eight of our fields show significant reddening [ E ( B  –  V ) ( g  –  i )  〉 0.20], which are targeted for follow-up studies of interstellar clouds. We find three systems (Q0059–0009, Q1033+2059 and Q2356+0029) with detectable galactic spectral emission, but no visible galaxy in imaging and no detectable absorption features. We speculate on the nature of these galaxies, which are strong candidates for dark galaxies and dwarf haloes.

Description: : Pyrosequencing of 16S rDNA is widely used to study microbial communities, and a rich set of software tools support this analysis. Pyrosequencing of protein-coding genes, which can help elucidate functional differences among microbial communities, significantly lags behind 16S rDNA in availability of sequence analysis software. In both settings, frequent homopolymer read errors inflate the estimation of microbial diversity, and de-noising is required to reduce that bias. Here we describe FunFrame, an R-based data-analysis pipeline that uses recently described algorithms to de-noise functional gene pyrosequences and performs ecological analysis on de-noised sequence data. The novelty of this pipeline is that it provides users a unified set of tools, adapted from disparate sources and designed for different applications, that can be used to examine a particular protein coding gene of interest. We evaluated FunFrame on functional genes from four PCR-amplified clones with sequence depths ranging from 9084 to 14 494 sequences. FunFrame produced from one to nine Operational Taxanomic Units for each clone, resulting in an error rate ranging from 0 to 0.18%. Importantly, FunFrame reduced spurious diversity while retaining more sequences than a commonly used de-noising method that discards sequences with frameshift errors. Availability: Software, documentation and a complete set of sample data files are available at http://faculty.www.umb.edu/jennifer.bowen/software/FunFrame.zip . Contact: Jennifer.Bowen@umb.edu Supplementary information: Supplementary data are available at Bioinformatics online.